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Mehl C, Mätz-Rensing K, Linde J, Struve B, Ismer G, van Hümmel C, Ulrich RG, Tomaso H. Case report: tularaemia in a white-handed gibbon ( Hylobates lar), Germany. Int J Vet Sci Med 2023; 11:121-125. [PMID: 38125824 PMCID: PMC10732199 DOI: 10.1080/23144599.2023.2264084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/05/2023] [Indexed: 12/23/2023] Open
Abstract
In 2021, a white-handed gibbon (Hylobates lar) succumbed to illness shortly after transfer from one zoo to another in Germany, due to Francisella tularensis subsp. holarctica infection. To determine the source of infection, whole genome sequencing of the gibbon-derived isolate was performed and wild pest rodents (and captive squirrels) from both zoos were screened for F. tularensis. The F. tularensis whole genome sequence obtained from the gibbon was closely related to previous subclade B.281 sequences obtained from hares from Baden-Wuerttemberg, the same region where the gibbon was first housed. However, F. tularensis DNA was detected in one Norway rat from the receiving zoo. Therefore, neither zoo can be excluded as the source of infection.
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Affiliation(s)
- Calvin Mehl
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases (INNT), Greifswald, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel- Riems, Greifswald, Germany
| | - Kerstin Mätz-Rensing
- German Primate Center GmbH (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jörg Linde
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute for Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | | | | | | | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases (INNT), Greifswald, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel- Riems, Greifswald, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute for Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
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Moawad AA, El-Adawy H, Linde J, Jost I, Tanja G, Katja H, Karsten D, Neubauer H, Monecke S, Tomaso H. Whole genome sequence-based analysis of Staphylococcus aureus isolated from bovine mastitis in Thuringia, Germany. Front Microbiol 2023; 14:1216850. [PMID: 37692386 PMCID: PMC10486899 DOI: 10.3389/fmicb.2023.1216850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/24/2023] [Indexed: 09/12/2023] Open
Abstract
Background Bovine mastitis is a common disease of dairy cattle causing major economic losses due to reduced yield and poor quality of milk worldwide. The current investigation aimed to gain insight into the genetic diversity, antimicrobial resistance profiles and virulence associated factors of Staphylococcus (S.) aureus isolated from clinical bovine mastitis in dairy farms in Thuringia, Germany. Methods Forty Staphylococcus aureus isolates collected from clinical bovine mastitis cases from 17 Thuringian dairy farms were phenotyped and genetically characterized using whole genome sequencing. Results Out of 40 S. aureus, 30 (75%) were confirmed as methicillin resistant isolates. The isolates showed elevated antimicrobial resistance against penicillin, tetracycline and oxacillin, i.e., 77.5, 77.5, and 75%, respectively. Lower resistance rates were found against moxifloxacin, ciprofloxacin, gentamicin and trimethoprim/sulfamethoxazole, i.e., 35, 35, 30, and 22.5%, respectively. While resistance against clindamycin and erythromycin was rarely found (5 and 2.5%, respectively). All isolates were susceptible to linezolid, teicoplanin, vancomycin, tigecycline, fosfomycin, fusidic acid and rifampicin. These isolates were further allocated into five different sequence types: ST398 (n = 31), ST1074 (n = 4), ST504 (n = 3), ST582 (CC15) (n = 1) and ST479 (n = 1). These isolates were also assigned to seven clusters with up to 100 SNP which has facilitated geographical mapping and epidemiological distribution in Thuringia. Strains belonging to ST398 were classified into clusters 1, 2, 3, 4 and 7. The isolates of ST504 were of cluster 5, those of ST1074 were belonging to cluster 6. Resistance genes blaZ, blaI and blaR associated with penicillin resistance were found in 32 (80%) strains, all except one were belonging to ST398. Methicillin resistance associated mecA was identified in 30 (96.8%) isolates of ST398. All tetracycline and erythromycin resistant isolates were of ST398, and all harbored both tetM and ermA. About 90.3% of tetracycline resistant isolates assigned to ST398 were also carrying tetK gene. The point mutations parC_S80F, gyrA_S84L and parC_S80Y in gyrA and parC associated with quinolone resistance were found in all phenotypically resistant isolates to ciprofloxacin and moxifloxacin (n = 14). Sixty-eight virulence genes were identified among isolates. Both lukD/E and lukM/F-PV-P83 were identified in 22.5% of isolates, all were non-ST398. Conclusion In this study, ST398 had the highest potential to cause disease and had a massive prevalence in bovine mastitis cases. Five different sequence types and seven clusters were identified in the federal state of Thuringia. The circulation of some clusters in the same region over several years shows the persistence of cluster-associated infection despite the intensive veterinary care. On the other hand, some regions had different clusters at the same year or in different consecutive years. Different sequence types and associated different clusters of S. aureus were geographically widely distributed among dairy farms in Thuringia. The findings of this study show that various clusters have the potential to spread over a large geographical scale. The detection of LA-MRSA on dairy farms, which is known for cabapility to widely spread among different groups of animals, humans and their environment urges for the implementation of national wide strategic programs. The identification of CA-MRSA among the isolates such as ST398 poses a significant risk for the transmission of such strains between animals and humans on dairy farms.
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Affiliation(s)
- Amira A. Moawad
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
- Animal Health Research Institute, Agriculture Research Center (ARC), Giza, Egypt
| | - Hosny El-Adawy
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
- Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Ines Jost
- Tiergesundheitsdienst der Thueringer Tierseuchenkasse, Jena, Germany
| | - Gärtner Tanja
- Tiergesundheitsdienst der Thueringer Tierseuchenkasse, Jena, Germany
| | - Hruschka Katja
- Tiergesundheitsdienst der Thueringer Tierseuchenkasse, Jena, Germany
| | - Donat Karsten
- Tiergesundheitsdienst der Thueringer Tierseuchenkasse, Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus Jena e.V., Jena, Germany
- Institute for Medical Microbiology and Virology, Dresden University Hospital, Dresden, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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Akinyemi KO, Fakorede CO, Linde J, Methner U, Wareth G, Tomaso H, Neubauer H. Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria. BMC Microbiol 2023; 23:164. [PMID: 37312043 DOI: 10.1186/s12866-023-02901-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/17/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Salmonella infections remain an important public health issue worldwide. Some serovars of non-typhoidal Salmonella (NTS) have been associated with bloodstream infections and gastroenteritis, especially in children in Sub-Saharan Africa with circulating S. enterica serovars with drug resistance and virulence genes. This study identified and verified the clonal relationship of Nigerian NTS strains isolated from humans, animals, and the environment. METHODS In total, 2,522 samples were collected from patients, animals (cattle and poultry), and environmental sources between December 2017 and May 2019. The samples were subjected to a standard microbiological investigation. All the isolates were identified using Microbact 24E, and MALDI-TOF MS. The isolates were serotyped using the Kauffmann-White scheme. Antibiotic susceptibility testing was conducted using the disc diffusion method and the Vitek 2 compact system. Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data. RESULTS Forty-eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified were S. Cotham (n = 17), S. Give (n = 16), S. Mokola (n = 6), S. Abony (n = 4), S. Typhimurium (n = 4), and S. Senftenberg (n = 1). All 48 Salmonella isolates carried intrinsic and acquired resistant genes such as aac.6…Iaa, mdf(A), qnrB, qnrB19 genes and golT, golS, pcoA, and silP, mediated by plasmid Col440I_1, incFIB.B and incFII. Between 100 and 118 virulence gene markers distributed across several Salmonella pathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. WGS revealed that strains of each Salmonella serovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. The dominant sequence types were S. Give ST516 and S. Cotham ST617. CONCLUSION We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. Strategies to control and prevent the spread of NTS in the context of one's health are essential to prevent possible outbreaks.
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Affiliation(s)
| | | | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, PO Box 13736, Toukh, Moshtohor, Egypt
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
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Thomas C, Methner U, Marz M, Linde J. Oxford nanopore technologies-a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella. Front Vet Sci 2023; 10:1178922. [PMID: 37323838 PMCID: PMC10267320 DOI: 10.3389/fvets.2023.1178922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteria of the genus Salmonella pose a major risk to livestock, the food economy, and public health. Salmonella infections are one of the leading causes of food poisoning. The identification of serovars of Salmonella achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by in silico serotyping has been established as an alternative method for serotyping and the detection of genetic markers for Salmonella. Until now, WGS data generated with Illumina sequencing are used to validate in silico serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 Salmonella strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the in silico serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, in silico serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for Salmonella in silico serotyping and genetic marker detection.
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Affiliation(s)
- Christine Thomas
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
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Linde J, Szabo I, Tausch SH, Deneke C, Methner U. Clonal relation between Salmonella enterica subspecies enterica serovar Dublin strains of bovine and food origin in Germany. Front Vet Sci 2023; 10:1081611. [PMID: 37303731 PMCID: PMC10248260 DOI: 10.3389/fvets.2023.1081611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/03/2023] [Indexed: 06/13/2023] Open
Abstract
Salmonella enterica subspecies enterica serovar Dublin (S. Dublin) is a host-adapted serovar causing enteritis and/or systemic diseases in cattle. As the serovar is not host-restricted, it may cause infections in other animals, including humans with severe illness and higher mortality rates than other non-typhoidal serovars. As human infections are mainly caused by contaminated milk, milk products and beef, information on the genetic relationship of S. Dublin strains from cattle and food should be evaluated. Whole-genome sequencing (WGS) of 144 S. Dublin strains from cattle and 30 strains from food origin was performed. Multilocus sequence typing (MLST) revealed mostly sequence type ST-10 from both, cattle and food isolates. In total, 14 of 30 strains from food origin were clonally related to at least one strain from cattle, as detected by core-genome single nucleotide polymorphisms typing as well as core-genome MLST. The remaining 16 foodborne strains fit into the genome structure of S. Dublin in Germany without outliers. WGS proved to be a powerful tool not only to gain information on the epidemiology of Salmonella strains but also to detect clonal relations between organisms isolated from different stages of production. This study has shown a high genetic correlation between S. Dublin strains from cattle and food and, therefore, the potential to cause human infections. S. Dublin strains of both origins share an almost identical set of virulence factors, emphasizing their potential to cause severe clinical manifestations in animals, but also in humans and thus the need for effective control of S. Dublin in a farm-to-fork strategy.
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Affiliation(s)
- Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Istvan Szabo
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
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Linde J, Brangsch H, Hölzer M, Thomas C, Elschner MC, Melzer F, Tomaso H. Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis. BMC Genomics 2023; 24:258. [PMID: 37173617 PMCID: PMC10182678 DOI: 10.1186/s12864-023-09343-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Bacterial epidemiology needs to understand the spread and dissemination of strains in a One Health context. This is important for highly pathogenic bacteria such as Bacillus anthracis, Brucella species, and Francisella tularensis. Whole genome sequencing (WGS) has paved the way for genetic marker detection and high-resolution genotyping. While such tasks are established for Illumina short-read sequencing, Oxford Nanopore Technology (ONT) long-read sequencing has yet to be evaluated for such highly pathogenic bacteria with little genomic variations between strains. In this study, three independent sequencing runs were performed using Illumina, ONT flow cell version 9.4.1, and 10.4 for six strains of each of Ba. anthracis, Br. suis and F. tularensis. Data from ONT sequencing alone, Illumina sequencing alone and two hybrid assembly approaches were compared. RESULTS As previously shown, ONT produces ultra-long reads, while Illumina produces short reads with higher sequencing accuracy. Flow cell version 10.4 improved sequencing accuracy over version 9.4.1. The correct (sub-)species were inferred from all tested technologies, individually. Moreover, the sets of genetic markers for virulence, were almost identical for the respective species. The long reads of ONT allowed to assemble not only chromosomes of all species to near closure, but also virulence plasmids of Ba. anthracis. Assemblies based on nanopore data alone, Illumina data alone, and both hybrid assemblies correctly detected canonical (sub-)clades for Ba. anthracis and F. tularensis as well as multilocus sequence types for Br. suis. For F. tularensis, high-resolution genotyping using core-genome MLST (cgMLST) and core-genome Single-Nucleotide-Polymorphism (cgSNP) typing produced highly comparable results between data from Illumina and both ONT flow cell versions. For Ba. anthracis, only data from flow cell version 10.4 produced similar results to Illumina for both high-resolution typing methods. However, for Br. suis, high-resolution genotyping yielded larger differences comparing Illumina data to data from both ONT flow cell versions. CONCLUSIONS In summary, combining data from ONT and Illumina for high-resolution genotyping might be feasible for F. tularensis and Ba. anthracis, but not yet for Br. suis. The ongoing improvement of nanopore technology and subsequent data analysis may facilitate high-resolution genotyping for all bacteria with highly stable genomes in future.
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Affiliation(s)
- Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany.
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Christine Thomas
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Mandy C Elschner
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
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Abdel-Glil MY, Hotzel H, Tomaso H, Didelot X, Brandt C, Seyboldt C, Linde J, Schwarz S, Neubauer H, El-Adawy H. Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany. Front Vet Sci 2023; 9:1069062. [PMID: 36744226 PMCID: PMC9893283 DOI: 10.3389/fvets.2022.1069062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
Campylobacter fetus subsp. venerealis (Cfv) causes bovine genital campylobacteriosis (BGC), a World Organization for Animal Health (WOAH)-listed trade-relevant disease characterized by severe reproductive losses, such as infertility, early embryonic death and abortion in cattle. BGC has significant economic implications that have prompted several countries to adopt stringent eradication and surveillance measures to contain the disease. In Germany, there has been a low incidence of BGC cases over the past 28 years. This study aimed to illustrate the genomic diversity of German Cfv strains isolated from different federal states in Germany. This study analyzed 63 Cfv strains, collected between 1985 and 2015, by whole-genome sequencing and compared them with genome data of 91 international Cfv isolates. The phylogenetic analysis showed that the Cfv population is genetically conserved and has geographic clusters. In Germany, one phylogenetic lineage comprising all strains was identified. This German lineage was part of a subclade that probably emerged in the nineteenth century and diversified over time. The results of this study point to a non-recurrent cross-border introduction of Cfv in Germany. The BGC control interventions in Germany can be considered successful as no outbreaks were reported since 2015.
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Affiliation(s)
- Mostafa Y. Abdel-Glil
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany,Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany,Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, Egypt,*Correspondence: Mostafa Y. Abdel-Glil ✉
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Christian Brandt
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Christian Seyboldt
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Jörg Linde
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany,Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Hosny El-Adawy
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany,Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt,Hosny El-Adawy ✉
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García-Soto S, Linde J, Methner U. Epidemiological Analysis on the Occurrence of Salmonella enterica Subspecies enterica Serovar Dublin in the German Federal State Schleswig-Holstein Using Whole-Genome Sequencing. Microorganisms 2023; 11:microorganisms11010122. [PMID: 36677417 PMCID: PMC9863307 DOI: 10.3390/microorganisms11010122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
The cattle-adapted serovar Salmonella Dublin (S. Dublin) causes enteritis and systemic diseases in animals. In the German federal state Schleswig-Holstein, S. Dublin is the most important serovar in cattle indicating an endemic character of the infection. To gain information on dissemination and routes of infection, whole-genome sequencing (WGS) was used to explore the genetic traits of 78 S. Dublin strains collected over a period of six years. The phylogeny was analysed using core-genome single nucleotide polymorphisms (cgSNPs). Genomic clusters at 100, 15 and 1 cgSNPs were selected for molecular analysis. Important specific virulence determinants were detected in all strains but multidrug resistance in S. Dublin organisms was not found. Using 15 cgSNPs epidemiological links between herds were identified, clusters at 1 cgSNPs provided clear evidence on both persistence of S. Dublin at single farms in consecutive years and transmission of the organisms between herds in different distances. A possible risk factor for the repeated occurrence of S. Dublin in certain districts of Schleswig-Holstein might be the spreading of manure on pastures and grassland. Effective control of S. Dublin requires farm-specific analysis of the management supplemented by WGS of outbreak causing S. Dublin strains to clearly identify routes of infection.
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El-Adawy H, Hotzel H, García-Soto S, Tomaso H, Hafez HM, Schwarz S, Neubauer H, Linde J. Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis. Front Vet Sci 2023; 10:1092179. [PMID: 36875995 PMCID: PMC9978446 DOI: 10.3389/fvets.2023.1092179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Campylobacter (C.) jejuni is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of C. jejuni recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq® technology was used to sequence 66 C. jejuni isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. The isolates were assigned to 28 different sequence types and 11 clonal complexes. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0-26,540 SNPs) revealed a high genetic distinction between the isolates. Thirteen virulence-associated genes were identified in C. jejuni isolates. Most of the isolates harbored the genes flaA (83.3%) and flaB (78.8%). The wlaN gene associated with the Guillain-Barré syndrome was detected in nine (13.6%) isolates. The genes for resistance to ampicillin (bla OXA), tetracycline [tet(O)], neomycin [aph(3')-IIIa], streptomycin (aadE) and streptothricin (sat4) were detected in isolated C. jejuni using WGS. A gene cluster comprising the genes sat4, aph(3')-IIIa and aadE was present in six isolates. The single point mutation T86I in the housekeeping gene gyrA conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. An assortment of 13 β-lactam resistance genes (bla OXA variants) was detected in 58 C. jejuni isolates. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. Six isolates harbored a pTet-like plasmid-borne contig which carries the tet(O) gene. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of C. jejuni. Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection.
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Affiliation(s)
- Hosny El-Adawy
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany.,Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Silvia García-Soto
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Hafez M Hafez
- Institute of Poultry Diseases, Free University Berlin, Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Veterinary Centre of Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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10
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Holzer K, Wareth G, El-Diasty M, Abdel-Hamid NH, Hamdy MER, Moustafa SA, Linde J, Bartusch F, Abdel-Glil MY, Sayour AE, Elbauomy EM, Elhadidy M, Melzer F, Beyer W. Tracking the distribution, genetic diversity and lineage of Brucella melitensis recovered from humans and animals in Egypt based on core-genome SNP analysis and in silico MLVA-16. Transbound Emerg Dis 2022; 69:3952-3963. [PMID: 36383491 DOI: 10.1111/tbed.14768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/07/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Brucellosis is one of the most common neglected zoonotic diseases globally, with a public health significance and a high economic loss in the livestock industry caused by the bacteria of the genus Brucella. In this study, 136 Egyptian Brucella melitensis strains isolated from animals and humans between 2001 and 2020 were analysed by examining the whole-core-genome single-nucleotide polymorphism (cgSNP) in comparison to the in silico multilocus variable number of tandem repeat analysis (MLVA-16). Almost all Egyptian isolates were belonging to the West Mediterranean clade, except two isolates from buffalo and camel were belonging to the American and East Mediterranean clades, respectively. A significant correlation between the human case of brucellosis and the possible source of infection from animals was found. It seems that several outbreak strains already existing for many years have been spread over long distances and between many governorates. The cgSNP analysis, in combination with epidemiological metadata, allows a better differentiation than the MLVA-16 genotyping method and, hence, the source definition and tracking of outbreak strains. The MLVA based on the currently used 16 markers is not suitable for this task. Our results revealed 99 different cgSNP genotypes with many different outbreak strains, both older and widely distributed ones and rather newly introduced ones as well. This indicates several different incidents and sources of infections, probably by imported animals from other countries to Egypt. Comparing our panel of isolates to public databases by cgSNP analysis, the results revealed near relatives from Italy. Moreover, near relatives from the United States, France, Austria and India were found by in silico MLVA.
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Affiliation(s)
- Katharina Holzer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Gamal Wareth
- Friedrich-Loeffler Institut, Institute for Bacterial Infections and Zoonoses, Jena, Germany.,Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh, Moshtohor, Egypt
| | - Mohamed El-Diasty
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Nour H Abdel-Hamid
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Mahmoud E R Hamdy
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Shawky A Moustafa
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh, Moshtohor, Egypt
| | - Jörg Linde
- Friedrich-Loeffler Institut, Institute for Bacterial Infections and Zoonoses, Jena, Germany
| | - Felix Bartusch
- IT Center (ZDV), High-Performance and Cloud Computing Group, University of Tuebingen, Tuebingen, Germany
| | - Mostafa Y Abdel-Glil
- Friedrich-Loeffler Institut, Institute for Bacterial Infections and Zoonoses, Jena, Germany
| | - Ashraf E Sayour
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Essam M Elbauomy
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Falk Melzer
- Friedrich-Loeffler Institut, Institute for Bacterial Infections and Zoonoses, Jena, Germany
| | - Wolfgang Beyer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
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11
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Brangsch H, Saqib M, Sial AUR, Melzer F, Linde J, Elschner MC. Sequencing-Based Genotyping of Pakistani Burkholderia mallei Strains: A Useful Way for Investigating Glanders Outbreaks. Pathogens 2022; 11:pathogens11060614. [PMID: 35745468 PMCID: PMC9227068 DOI: 10.3390/pathogens11060614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/05/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
Burkholderia (B.) mallei is a host-adapted equine pathogen that causes glanders, a re-emerging zoonotic disease, which is endemic in Pakistan and other developing countries and seriously impacts the global equine movement. Due to globalization, the geographical restriction of diseases vanishes and the lack of awareness of and experience with eradicated diseases in industrialized countries also promotes the re-introduction of infections in these regions. Owing to the high equine population, the Pakistani province Punjab is a potential hotspot where several glanders outbreaks have been seen over last two decades. For determining the genomic diversity of B. mallei in this and other equine-populated prefectures, the genomes of 19 B. mallei strains isolated between 1999 and 2020 in different locations were sequenced and their genotypes were determined. Particularly, for genetically highly homogenous pathogens like B. mallei genotyping techniques require a high discriminatory power for enabling differentiation on the strain level. Thus, core-genome single nucleotide polymorphism (cgSNP) analysis was applied for distinguishing the highly similar strains. Furthermore, a whole-genome sequence-based core genome multi locus sequence typing (cgMLST) scheme, specific to B. mallei, was developed and additionally applied to the data. It was found that B. mallei genotypes in Pakistan persisted over time and space and genotype clusters preferred connection with a time point rather than the place of isolation, probably due to frequent equine movement, which promotes the spread of glanders. The cgMLST approach proved to work in accord with SNP typing and may help to investigate future glanders outbreaks.
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Affiliation(s)
- Hanka Brangsch
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743 Jena, Thuringia, Germany; (F.M.); (J.L.); (M.C.E.)
- Correspondence:
| | - Muhammad Saqib
- Veterinary Preventive Medicine and Public Health Laboratory, Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad 38000, Pakistan;
| | - Awais ur Rehman Sial
- Department of Clinical Studies, Faculty of Veterinary and Animal Science, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi 46000, Pakistan;
| | - Falk Melzer
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743 Jena, Thuringia, Germany; (F.M.); (J.L.); (M.C.E.)
| | - Jörg Linde
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743 Jena, Thuringia, Germany; (F.M.); (J.L.); (M.C.E.)
| | - Mandy Carolina Elschner
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743 Jena, Thuringia, Germany; (F.M.); (J.L.); (M.C.E.)
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12
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Wareth G, Linde J, Hammer P, Pletz MW, Neubauer H, Sprague LD. WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in Klebsiella pneumoniae Isolates from Powdered Milk Produced in Germany. Microorganisms 2022; 10:microorganisms10030564. [PMID: 35336140 PMCID: PMC8956024 DOI: 10.3390/microorganisms10030564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
The emergence of Klebsiella pneumoniae (K. pneumoniae) in German healthcare is worrying. It is not well-investigated in the veterinary world and food chains. In the current study, antibiotic susceptibility profiles of 24 K. pneumoniae strains isolated from powdered milk samples produced in Germany were investigated by a microdilution test. Next-generation sequencing (NGS) was applied to identify genomic determinants for antimicrobial resistance (AMR), virulence-associated genes and plasmids replicons. All isolates were susceptible to the majority (14/18) of tested antibiotics. Resistance to colistin, fosfomycin, chloramphenicol and piperacillin was found. The ambler class A ß-lactamase, blaSHV variants were identified in all isolates, of which blaSHV-187 was most prevalent and found in 50% of isolates. Single-nucleotide-variants of oqxA and oqxB conferring resistance to phenicol/quinolone were found in all isolates, and the oqxB17 was the most prevalent found in 46% of isolates. 67% of isolates harbored fosA genes; however, only one was fosfomycin-resistant. Two isolates harbored genes conferring resistance to colistin, despite being susceptible. The majority of identified virulome genes were iron uptake siderophores. Two enterobactins (entB, fepC), six adherence-related genes belonging to E. coli common pilus (ECP) and one secretion system (ompA gene) were found in all isolates. In contrast, yersiniabactin was found in two isolates. One ST23 strain was susceptible to all tested antibiotics, and harbored determinants discriminatory for hypervirulent strains, e.g., aerobactin, salmochelin, yersiniabactin, enterobactin and regulator of mucoid phenotype A genes that are highly associated with hypervirulent K. pneumoniae. The IncF plasmid family was found in all strains, while almost half of the isolates harbored Col440I-type plasmids and nine isolates harbored various Inc-type plasmids. The presence of K. pneumoniae carrying different resistomes and major virulent specific virulomes in powdered milk samples is alarming. This could threaten public health, particularly of neonates and infants consuming dried milk.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena University, 07743 Jena, Germany;
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
- Correspondence:
| | - Jörg Linde
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
| | - Philipp Hammer
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany;
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena University, 07743 Jena, Germany;
- Research Campus Infectognostics, Philosophenweg 7, 07743 Jena, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
| | - Lisa D. Sprague
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
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13
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Brangsch H, Golovko A, Pinchuk N, Deriabin O, Kyselova T, Linde J, Melzer F, Elschner MC. Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques. Microorganisms 2022; 10:microorganisms10020461. [PMID: 35208915 PMCID: PMC8875922 DOI: 10.3390/microorganisms10020461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining long- and short-read next-generation sequencing techniques, highly accurate genomes were reconstructed, enabling detailed in silico genotyping. Thus, the strains could be assigned to the Tsiankovskii subgroup of the “TransEurAsia” clade, which is commonly found in this region. Their high genetic similarity suggests that the four strains are members of the endemic population whose progenitor was once introduced in the Ukraine and bordering regions. This study provides information on B. anthracis strains from a region where there is little knowledge of the local population, thereby adding to the picture of global B. anthracis genotype distribution. We also emphasize the importance of surveillance and prevention methods regarding anthrax outbreaks, as other studies predicted a higher number of cases in the future due to global warming.
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Affiliation(s)
- Hanka Brangsch
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
- Correspondence:
| | - Anatolii Golovko
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Nataliia Pinchuk
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Oleg Deriabin
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Tetiana Kyselova
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Jörg Linde
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| | - Falk Melzer
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| | - Mandy Carolina Elschner
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
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14
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Hölzer M, Escobar-Zepeda A, Linde J, Horn F. Editorial: The Transition Era to New Sequencing Technologies and Their Application to Integrative Omics in Molecular Surveillance. Front Genet 2022; 13:840782. [PMID: 35251137 PMCID: PMC8889007 DOI: 10.3389/fgene.2022.840782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Martin Hölzer
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
- *Correspondence: Martin Hölzer,
| | | | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Fabian Horn
- Federal Office of Consumer Protection and Food Safety (BVL), Braunschweig, Germany
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15
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Abdel-Glil MY, Thomas P, Linde J, Jolley KA, Harmsen D, Wieler LH, Neubauer H, Seyboldt C. Establishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens. Microbiol Spectr 2021; 9:e0053321. [PMID: 34704797 PMCID: PMC8549748 DOI: 10.1128/spectrum.00533-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/16/2021] [Indexed: 12/31/2022] Open
Abstract
Clostridium perfringens is a spore-forming anaerobic pathogen responsible for a variety of histotoxic and intestinal infections in humans and animals. High-resolution genotyping aiming to identify bacteria at strain level has become increasingly important in modern microbiology to understand pathogen transmission pathways and to tackle infection sources. This study aimed at establishing a publicly available genome-wide multilocus sequence-typing (MLST) scheme for C. perfringens. A total of 1,431 highly conserved core genes (1.34 megabases; 50% of the reference genome genes) were indexed for a core genome-based MLST (cgMLST) scheme for C. perfringens. The scheme was applied to 282 ecologically and geographically diverse genomes, showing that the genotyping results of cgMLST were highly congruent with the core genome-based single-nucleotide-polymorphism typing in terms of resolution and tree topology. In addition, the cgMLST provided a greater discrimination than classical MLST methods for C. perfringens. The usability of the scheme for outbreak analysis was confirmed by reinvestigating published outbreaks of C. perfringens-associated infections in the United States and the United Kingdom. In summary, a publicly available scheme and an allele nomenclature database for genomic typing of C. perfringens have been established and can be used for broad-based and standardized epidemiological studies. IMPORTANCE Global epidemiological surveillance of bacterial pathogens is enhanced by the availability of standard tools and sharing of typing data. The use of whole-genome sequencing has opened the possibility for high-resolution characterization of bacterial strains down to the clonal and subclonal levels. Core genome multilocus sequence typing is a robust system that uses highly conserved core genes for deep genotyping. The method has been successfully and widely used to describe the epidemiology of various bacterial species. Nevertheless, a cgMLST typing scheme for Clostridium perfringens is currently not publicly available. In this study, we (i) developed a cgMLST typing scheme for C. perfringens, (ii) evaluated the performance of the scheme on different sets of C. perfringens genomes from different hosts and geographic regions as well as from different outbreak situations, and, finally, (iii) made this scheme publicly available supported by an allele nomenclature database for global and standard genomic typing.
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Affiliation(s)
- Mostafa Y. Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
- Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia Province, Egypt
| | - Prasad Thomas
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Keith A. Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Dag Harmsen
- Department of Periodontology and Operative Dentistry, University Hospital Muenster, Muenster, Germany
| | | | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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16
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Radosa S, Sprague JL, Lau S, Tóth R, Linde J, Krüger T, Sprenger M, Kasper L, Westermann M, Kniemeyer O, Hube B, Brakhage AA, Gácser A, Hillmann F. Cover Image: The fungivorous amoeba
Protostelium aurantium
targets redox homeostasis and cell wall integrity during intracellular killing of
Candida parapsilosis
(Cellular Microbiology 11/2021). Cell Microbiol 2021. [DOI: 10.1111/cmi.13396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Holzer K, El-Diasty M, Wareth G, Abdel-Hamid NH, Hamdy MER, Moustafa SA, Linde J, Bartusch F, Sayour AE, Elbauomy EM, Elhadidy M, Melzer F, Beyer W. Tracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16. Microorganisms 2021; 9:microorganisms9091942. [PMID: 34576838 PMCID: PMC8469952 DOI: 10.3390/microorganisms9091942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Brucellosis, caused by the bacteria of the genus Brucella, is one of the most neglected common zoonotic diseases globally with a public health significance and a high economic loss among the livestock industry worldwide. Since little is known about the distribution of B. abortus in Egypt, a total of 46 B. abortus isolates recovered between 2012–2020, plus one animal isolate from 2006, were analyzed by examining the whole core genome single nucleotide polymorphism (cgSNP) in comparison to the in silico multilocus variable number of tandem repeat analysis (MLVA). Both cgSNP analysis and MLVA revealed three clusters and one isolate only was distantly related to the others. One cluster identified a rather widely distributed outbreak strain which is repeatedly occurring for at least 16 years with marginal deviations in cgSNP analysis. The other cluster of isolates represents a rather newly introduced outbreak strain. A separate cluster comprised RB51 vaccine related strains, isolated from aborted material. The comparison with MLVA data sets from public databases reveals one near relative from Argentina to the oldest outbreak strain and a related strain from Spain to a newly introduced outbreak strain in Egypt. The distantly related isolate matches with a strain from Portugal in the MLVA profile. Based on cgSNP analysis the oldest outbreak strain clusters with strains from the UK. Compared to the in silico analysis of MLVA, cgSNP analysis using WGS data provides a much higher resolution of genotypes and, when correlated to the associated epidemiological metadata, cgSNP analysis allows the differentiation of outbreaks by defining different outbreak strains. In this respect, MLVA data are error-prone and can lead to incorrect interpretations of outbreak events.
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Affiliation(s)
- Katharina Holzer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany;
- Correspondence: ; Tel.: +49-711-4592-2428
| | - Mohamed El-Diasty
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Gamal Wareth
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt; (G.W.); (S.A.M.)
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.)
| | - Nour H. Abdel-Hamid
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Mahmoud E. R. Hamdy
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Shawky A. Moustafa
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt; (G.W.); (S.A.M.)
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.)
| | - Felix Bartusch
- High-Performance and Cloud Computing Group, IT Center (ZDV), University of Tuebingen, Waechterstrasse 76, 72074 Tübingen, Germany;
| | - Ashraf E. Sayour
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Essam M. Elbauomy
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt;
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.)
| | - Wolfgang Beyer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany;
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18
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Radosa S, Sprague JL, Lau SH, Tóth R, Linde J, Krüger T, Sprenger M, Kasper L, Westermann M, Kniemeyer O, Hube B, Brakhage AA, Gácser A, Hillmann F. The fungivorous amoeba Protostelium aurantium targets redox homeostasis and cell wall integrity during intracellular killing of Candida parapsilosis. Cell Microbiol 2021; 23:e13389. [PMID: 34460149 DOI: 10.1111/cmi.13389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 03/08/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022]
Abstract
Predatory interactions among microbes are major evolutionary driving forces for biodiversity. The fungivorous amoeba Protostelium aurantium has a wide fungal food spectrum including foremost pathogenic members of the genus Candida. Here we show that upon phagocytic ingestion by the amoeba, Candida parapsilosis is confronted with an oxidative burst and undergoes lysis within minutes of processing in acidified phagolysosomes. On the fungal side, a functional genomic approach identified copper and redox homeostasis as primary targets of amoeba predation, with the highly expressed copper exporter gene CRP1 and the peroxiredoxin gene PRX1 contributing to survival when encountered with P. aurantium. The fungicidal activity was largely retained in intracellular vesicles of the amoebae. Following their isolation, the content of these vesicles induced immediate killing and lysis of C. parapsilosis in vitro. Proteomic analysis identified 56 vesicular proteins from P. aurantium. Although completely unknown proteins were dominant, many of them could be categorised as hydrolytic enzymes targeting the fungal cell wall, indicating that fungal cell wall structures are under selection pressure by predatory phagocytes in natural environments. TAKE AWAY: The amoeba Protostelium aurantium feeds on fungi, such as Candida parapsilosis. Ingested yeast cells are exposed to reactive oxygen species. A copper exporter and a peroxiredoxin contribute to fungal defence. Yeast cells undergo intracellular lysis. Lysis occurs via a cocktail of hydrolytic enzymes from intracellular vesicles.
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Affiliation(s)
- Silvia Radosa
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Jakob L Sprague
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Siu-Hin Lau
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Renáta Tóth
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Jörg Linde
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Marcel Sprenger
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Lydia Kasper
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | | | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Bernhard Hube
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Attila Gácser
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
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19
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Wareth G, Linde J, Hammer P, Nguyen NH, Nguyen TNM, Splettstoesser WD, Makarewicz O, Neubauer H, Sprague LD, Pletz MW. Corrigendum to "Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii isolates from Germany and Vietnam" [International Journal of Antimicrobial Agents, Volume 56, Issue 4, October 2020, 106127]. Int J Antimicrob Agents 2021; 58:106407. [PMID: 34325973 DOI: 10.1016/j.ijantimicag.2021.106407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany; Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.
| | - Jörg Linde
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Philipp Hammer
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Kiel, Germany
| | - Ngoc H Nguyen
- The Center of Training and Direction of Healthcare Activities, General Hospital of Phutho, Vietnam; Department of Health, General Hospital of Phutho, Phutho, Vietnam
| | - Tuan N M Nguyen
- The Center of Training and Direction of Healthcare Activities, General Hospital of Phutho, Vietnam
| | - Wolf D Splettstoesser
- Department of Microbiology & Hygiene, LADR GmbH, Medical Laboratory Braunschweig, Germany
| | - Oliwia Makarewicz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany; Research Campus Infectognostics, Jena, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Lisa D Sprague
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany; Research Campus Infectognostics, Jena, Germany
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20
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Abdel-Glil MY, Thomas P, Linde J, Busch A, Wieler LH, Neubauer H, Seyboldt C. Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential. Sci Rep 2021; 11:6756. [PMID: 33762628 PMCID: PMC7991664 DOI: 10.1038/s41598-021-86148-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/11/2021] [Indexed: 12/16/2022] Open
Abstract
Clostridium perfringens causes a plethora of devastating infections, with toxin production being the underlying mechanism of pathogenicity in various hosts. Genomic analyses of 206 public-available C. perfringens strains´ sequence data identified a substantial degree of genomic variability in respect to episome content, chromosome size and mobile elements. However, the position and order of the local collinear blocks on the chromosome showed a considerable degree of preservation. The strains were divided into five stable phylogroups (I–V). Phylogroup I contained human food poisoning strains with chromosomal enterotoxin (cpe) and a Darmbrand strain characterized by a high frequency of mobile elements, a relatively small genome size and a marked loss of chromosomal genes, including loss of genes encoding virulence traits. These features might correspond to the adaptation of these strains to a particular habitat, causing human foodborne illnesses. This contrasts strains that belong to phylogroup II where the genome size points to the acquisition of genetic material. Most strains of phylogroup II have been isolated from enteric lesions in horses and dogs. Phylogroups III, IV and V are heterogeneous groups containing a variety of different strains, with phylogroup III being the most abundant (65.5%). In conclusion, C. perfringens displays five stable phylogroups reflecting different disease involvements, prompting further studies on the evolution of this highly important pathogen.
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Affiliation(s)
- Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany. .,Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia Province, Egypt.
| | - Prasad Thomas
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany.,Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany
| | - Anne Busch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany.,Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Lothar H Wieler
- Robert Koch-Institut, Nordufer 20, 13353, Berlin, Germany.,Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität, Robert-von-Ostertag-Str. 7-13, Building 35, 14163, Berlin, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany.
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21
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Uelze L, Becker N, Borowiak M, Busch U, Dangel A, Deneke C, Fischer J, Flieger A, Hepner S, Huber I, Methner U, Linde J, Pietsch M, Simon S, Sing A, Tausch SH, Szabo I, Malorny B. Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany. Front Microbiol 2021; 12:626941. [PMID: 33643254 PMCID: PMC7902525 DOI: 10.3389/fmicb.2021.626941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/21/2021] [Indexed: 02/03/2023] Open
Abstract
Despite extensive monitoring programs and preventative measures, Salmonella spp. continue to cause tens of thousands human infections per year, as well as many regional and international food-borne outbreaks, that are of great importance for public health and cause significant socio-economic costs. In Germany, salmonellosis is the second most common cause of bacterial diarrhea in humans and is associated with high hospitalization rates. Whole-genome sequencing (WGS) combined with data analysis is a high throughput technology with an unprecedented discriminatory power, which is particularly well suited for targeted pathogen monitoring, rapid cluster detection and assignment of possible infection sources. However, an effective implementation of WGS methods for large-scale microbial pathogen detection and surveillance has been hampered by the lack of standardized methods, uniform quality criteria and strategies for data sharing, all of which are essential for a successful interpretation of sequencing data from different sources. To overcome these challenges, the national GenoSalmSurv project aims to establish a working model for an integrated genome-based surveillance system of Salmonella spp. in Germany, based on a decentralized data analysis. Backbone of the model is the harmonization of laboratory procedures and sequencing protocols, the implementation of open-source bioinformatics tools for data analysis at each institution and the establishment of routine practices for cross-sectoral data sharing for a uniform result interpretation. With this model, we present a working solution for cross-sector interpretation of sequencing data from different sources (such as human, veterinarian, food, feed and environmental) and outline how a decentralized data analysis can contribute to a uniform cluster detection and facilitate outbreak investigations.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Natalie Becker
- Department of Food, Feed and Commodities, Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Alexandra Dangel
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Antje Flieger
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Hepner
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Michael Pietsch
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sandra Simon
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Istvan Szabo
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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22
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Müller E, Hotzel H, Linde J, Hänel I, Tomaso H. Antimicrobial Resistance and in silico Virulence Profiling of Aliarcobacter butzleri Strains From German Water Poultry. Front Microbiol 2020; 11:617685. [PMID: 33381106 PMCID: PMC7767855 DOI: 10.3389/fmicb.2020.617685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Aliarcobacter butzleri is an emerging foodborne and zoonotic pathogen that is usually transmitted via contaminated food or water. A. butzleri is not only the most prevalent Aliarcobacter species, it is also closely related to thermophilic Campylobacter, which have shown increasing resistance in recent years. Therefore, it is important to assess its resistance and virulence profiles. In this study, 45 Aliarcobacter butzleri strains from water poultry farms in Thuringia, Germany, were subjected to an antimicrobial susceptibility test using the gradient strip diffusion method and whole-genome sequencing. In the phylogenetic analysis, the genomes of the German strains showed high genetic diversity. Thirty-three isolates formed 11 subgroups containing two to six strains. The antimicrobial susceptibility testing showed that 32 strains were resistant to erythromycin, 26 to doxycycline, and 20 to tetracycline, respectively. Only two strains were resistant to ciprofloxacin, while 39 strains were resistant to streptomycin. The in silico prediction of the antimicrobial resistance profiles identified a large repertoire of potential resistance mechanisms. A strong correlation between a gyrA point mutation (Thr-85-Ile) and ciprofloxacin resistance was found in 11 strains. A partial correlation was observed between the presence of the bla3 gene and ampicillin resistance. In silico virulence profiling revealed a broad spectrum of putative virulence factors, including a complete lipid A cluster in all studied genomes.
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Affiliation(s)
- Eva Müller
- Institute of Bacterial Infections and Zoonoses (IBIZ), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses (IBIZ), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses (IBIZ), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
| | - Ingrid Hänel
- Institute of Bacterial Infections and Zoonoses (IBIZ), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses (IBIZ), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
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23
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Linde J, Homeier-Bachmann T, Dangel A, Riehm JM, Sundell D, Öhrman C, Forsman M, Tomaso H. Genotyping of Francisella tularensis subsp. holarctica from Hares in Germany. Microorganisms 2020; 8:microorganisms8121932. [PMID: 33291395 PMCID: PMC7761992 DOI: 10.3390/microorganisms8121932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 02/04/2023] Open
Abstract
Francisella tularensis is the causative agent of the zoonotic disease tularemia. In Germany, most human infections are caused by contact with infected hares. The aim of this study was to characterize Francisella tularensis subsp. holarctica strains isolated from hares in Germany and to develop bioinformatics tools to analyze their genetic relatedness. In total, 257 German isolates-obtained mainly from hares (n = 233), other vertebrate animals, and ticks, but also from humans (n = 3)-were analyzed within this study. Publically available sequence data from 49 isolates were used to put our isolates into an epidemiological context and to compare isolates from natural foci and humans. Whole-genome sequences were analyzed using core-genome Multi-Locus-Sequence-Typing, canonical Single Nucleotide Polymorphism (SNP) typing and whole-genome SNP typing. An overall conformity of genotype clustering between the typing methods was found, albeit with a lower resolution for canonical single SNP typing. The subclade distribution, both on local and national levels, among strains from humans and hares was similar, suggesting circulation of the same genotypes both in animals and humans. Whilst close to identical isolates of the same subclade were found distributed over large areas, small geographical foci often harbored members of different subclades. In conclusion, although genomic high-resolution typing was shown to be robust, reproducible and allowed the identification of highly closely related strains, genetic profiling alone is not always conclusive for epidemiological linkage of F. tularensis strains.
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Affiliation(s)
- Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: ; Tel.: +49-3641-804-2320
| | - Timo Homeier-Bachmann
- Institute of Epidemiology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany;
| | - Alexandra Dangel
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, 85764 Oberschleißheim, Germany; (A.D.); (J.M.R.)
| | - Julia M. Riehm
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, 85764 Oberschleißheim, Germany; (A.D.); (J.M.R.)
| | - David Sundell
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), SE-901 82 Umeå, Sweden; (D.S.); (C.Ö.); (M.F.)
| | - Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), SE-901 82 Umeå, Sweden; (D.S.); (C.Ö.); (M.F.)
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), SE-901 82 Umeå, Sweden; (D.S.); (C.Ö.); (M.F.)
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
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24
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Gruenewald T, Pellissier V, Philipp E, Wolfensteller K, Hoffmann I, Zabel R, Ackermann G, Pöge A, Linde J, Lakowa N. Antimicrobial resistance in Helicobacter pylori – State-wide surveillance from the Saxony antibiotic network project (ABNW). Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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25
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Lakowa N, Pellissier V, Ackermann G, Zabel R, Hoffmann I, Philipp E, Wolfensteller K, Pöge A, Linde J, Gruenewald T. Antimicrobial resistance to rescue substances in Gram-negative ESKAPE pathogens – State-wide surveillance from the Saxony antibiotic network project. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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26
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Abdel-Glil MY, Hotzel H, Tomaso H, Linde J. Phylogenomic Analysis of Campylobacter fetus Reveals a Clonal Structure of Insertion Element IS Cfe1 Positive Genomes. Front Microbiol 2020; 11:585374. [PMID: 33281781 PMCID: PMC7688749 DOI: 10.3389/fmicb.2020.585374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023] Open
Abstract
Subspecies of the species Campylobacter fetus are associated with specific host niches including mammals and reptiles. Campylobacter fetus subsp. fetus is a zoonotic pathogen infecting humans. Infections can vary from an acute intestinal illness to severe systemic infections, with sheep and cattle as major reservoirs. In contrast, Campylobacter fetus subsp. venerealis causes bovine genital campylobacteriosis, which leads to abortion in cattle and a high economic burden for the farmers. Therefore, high-quality molecular subtyping is indispensable for interventional epidemiology. We used whole-genome sequencing (WGS) data of 283 Campylobacter fetus strains from 18 countries and compared several methods for Campylobacter fetus subtyping, including WGS, multilocus sequence typing, PCR assays, and the presence of the insertion element ISCfe1. We identified a highly clonal clade (designated as clade 1) that harbors the insertion sequence ISCfe1. The presence of this insertion sequence is an essential diagnostic tool for the identification of the subspecies Campylobacter fetus subsp. venerealis, serving as a target for several PCR assays. However, we have found a high sequence variability for the ISCfe1 besides the presence of ISCfe1-paralogues in certain other genomes (n = 7) which may cause incorrect diagnostic results. Clade 1 seems to be the cattle-specific clade of this species. We propose that only this clade might be designated as Campylobacter fetus subsp. venerealis as it harbors the ISCfe1 marker sequence, which is a major target for molecular methods currently used for Campylobacter fetus subspecies identification. Fostering this proposal, we defined eleven stable nucleotide markers specific for this clade. Additionally, we developed a bioinformatics toolbox for the fast identification of this clade based on WGS data. In conclusion, our results demonstrate that WGS can be used for Campylobacter fetus subtyping overcoming limitations of current PCR and MLST protocols.
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Affiliation(s)
- Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany.,Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Ash Sharqiyah, Egypt
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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27
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Seelbinder B, Wallstabe J, Marischen L, Weiss E, Wurster S, Page L, Löffler C, Bussemer L, Schmitt AL, Wolf T, Linde J, Cicin-Sain L, Becker J, Kalinke U, Vogel J, Panagiotou G, Einsele H, Westermann AJ, Schäuble S, Loeffler J. Triple RNA-Seq Reveals Synergy in a Human Virus-Fungus Co-infection Model. Cell Rep 2020; 33:108389. [PMID: 33207195 DOI: 10.1016/j.celrep.2020.108389] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
High-throughput RNA sequencing (RNA-seq) is routinely applied to study diverse biological processes; however, when performed separately on interacting organisms, systemic noise intrinsic to RNA extraction, library preparation, and sequencing hampers the identification of cross-species interaction nodes. Here, we develop triple RNA-seq to simultaneously detect transcriptomes of monocyte-derived dendritic cells (moDCs) infected with the frequently co-occurring pulmonary pathogens Aspergillus fumigatus and human cytomegalovirus (CMV). Comparing expression patterns after co-infection with those after single infections, our data reveal synergistic effects and mutual interferences between host responses to the two pathogens. For example, CMV attenuates the fungus-mediated activation of pro-inflammatory cytokines through NF-κB (nuclear factor κB) and NFAT (nuclear factor of activated T cells) cascades, while A. fumigatus impairs viral clearance by counteracting viral nucleic acid-induced activation of type I interferon signaling. Together, the analytical power of triple RNA-seq proposes molecular hubs in the differential moDC response to fungal/viral single infection or co-infection that contribute to our understanding of the etiology and, potentially, clearance of post-transplant infections.
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Affiliation(s)
- Bastian Seelbinder
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Julia Wallstabe
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Lothar Marischen
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Esther Weiss
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Sebastian Wurster
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany; The University of Texas MD Anderson Cancer Center, Department of Infectious Diseases, Infection Control and Employee Health, Houston, TX 77030, USA
| | - Lukas Page
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Claudia Löffler
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Lydia Bussemer
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Anna-Lena Schmitt
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Thomas Wolf
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Jörg Linde
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany
| | - Luka Cicin-Sain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Hannover-Braunschweig Site, 38124 Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH) Braunschweig, 38124 Braunschweig, Germany
| | - Jennifer Becker
- Institute for Experimental Infection Research, TWINCORE-Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE-Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), 07745 Jena, Germany; Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong S.A.R., China
| | - Hermann Einsele
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Alexander J Westermann
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Sascha Schäuble
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Juergen Loeffler
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany.
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Weiss E, Schlegel J, Terpitz U, Weber M, Linde J, Schmitt AL, Hünniger K, Marischen L, Gamon F, Bauer J, Löffler C, Kurzai O, Morton CO, Sauer M, Einsele H, Loeffler J. Reconstituting NK Cells After Allogeneic Stem Cell Transplantation Show Impaired Response to the Fungal Pathogen Aspergillus fumigatus. Front Immunol 2020; 11:2117. [PMID: 33013893 PMCID: PMC7511764 DOI: 10.3389/fimmu.2020.02117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/05/2020] [Indexed: 01/03/2023] Open
Abstract
Delayed natural killer (NK) cell reconstitution after allogeneic stem cell transplantation (alloSCT) is associated with a higher risk of developing invasive aspergillosis. The interaction of NK cells with the human pathogen Aspergillus (A.) fumigatus is mediated by the fungal recognition receptor CD56, which is relocated to the fungal interface after contact. Blocking of CD56 signaling inhibits the fungal mediated chemokine secretion of MIP-1α, MIP-1β, and RANTES and reduces cell activation, indicating a functional role of CD56 in fungal recognition. We collected peripheral blood from recipients of an allograft at defined time points after alloSCT (day 60, 90, 120, 180). NK cells were isolated, directly challenged with live A. fumigatus germ tubes, and cell function was analyzed and compared to healthy age and gender-matched individuals. After alloSCT, NK cells displayed a higher percentage of CD56brightCD16dim cells throughout the time of blood collection. However, CD56 binding and relocalization to the fungal contact side were decreased. We were able to correlate this deficiency to the administration of corticosteroid therapy that further negatively influenced the secretion of MIP-1α, MIP-1β, and RANTES. As a consequence, the treatment of healthy NK cells ex vivo with corticosteroids abrogated chemokine secretion measured by multiplex immunoassay. Furthermore, we analyzed NK cells regarding their actin cytoskeleton by Structured Illumination Microscopy (SIM) and flow cytometry and demonstrate an actin dysfunction of NK cells shown by reduced F-actin content after fungal co-cultivation early after alloSCT. This dysfunction remains until 180 days post-alloSCT, concluding that further actin-dependent cellular processes may be negatively influenced after alloSCT. To investigate the molecular pathomechansism, we compared CD56 receptor mobility on the plasma membrane of healthy and alloSCT primary NK cells by single-molecule tracking. The results were very robust and reproducible between tested conditions which point to a different molecular mechanism and emphasize the importance of proper CD56 mobility.
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Affiliation(s)
- Esther Weiss
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Würzburg, Germany
| | - Jan Schlegel
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Michael Weber
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Jörg Linde
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Anna-Lena Schmitt
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Würzburg, Germany
| | - Kerstin Hünniger
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany.,Institute for Hygiene and Microbiology, Julius-Maximilian-University, Würzburg, Germany
| | - Lothar Marischen
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Würzburg, Germany
| | - Florian Gamon
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Würzburg, Germany
| | - Joachim Bauer
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Würzburg, Germany
| | - Claudia Löffler
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Würzburg, Germany
| | - Oliver Kurzai
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany.,Institute for Hygiene and Microbiology, Julius-Maximilian-University, Würzburg, Germany
| | | | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Würzburg, Germany
| | - Juergen Loeffler
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Würzburg, Germany
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29
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Wareth G, Linde J, Hammer P, Nguyen NH, Nguyen TNM, Splettstoesser WD, Makarewicz O, Neubauer H, Sprague LD, Pletz MW. Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii isolates from Germany and Vietnam. Int J Antimicrob Agents 2020; 56:106127. [PMID: 32750418 DOI: 10.1016/j.ijantimicag.2020.106127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/02/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES This study aimed to combine in vitro phenotyping analysis and whole-genome-sequencing (WGS) to characterise the phenotype and genetic determinants associated with intrinsic resistance in 100 clinical and non-clinical Acinetobacter baumannii strains originating from Germany and Vietnam. Moreover, it aimed to assess whether powdered milk as a food source functions as a potential reservoir of antibiotic resistance and possesses similar antimicrobial resistance (AMR) genes as in clinical strains isolated from Germany. METHODS Antimicrobial susceptibility testing was performed using the broth microdilution method and the minimum inhibitory concentration (MIC) was determined for 18 antibiotics. The WGS data from all isolates were mapped to intrinsic genes known to be associated with phenotypic AMR. RESULTS The highest resistance frequency was observed for chloramphenicol (100%), followed by fosfomycin (96%) and cefotaxime (95%). The lowest resistant rates were observed for colistin (3%), trimethoprim/sulfamethoxazole (17%), tigecycline (19%), and amikacin (19%). Thirty-five percent of tested strains displayed resistance to at least one of the carbapenems. Resistance to fluoroquinolones, aminoglycosides, tigecycline, penicillins, trimethoprim/sulfamethoxazole, and fourth-generation cephalosporins was determined only in human strains. About one-quarter of isolates (24%) was multidrug-resistant (MDR) and all were of human origin. Among them, 16 isolates were extensively drug resistant (XDR) and 10 from those 16 isolates showed resistance to all tested antibiotics except colistin. In silico detection of intrinsic AMR genes revealed the presence of 36 β-lactamases and 24 non-β-lactamase resistance genes. Two colistin-resistant and 10 ertapenem-resistant strains were isolated from powdered milk produced in Germany. Thirty-eight AMR genes associated with resistance to antibiotics were found in isolates recovered from milk powder. Several resistance mechanisms towards many classes of antibiotics existed in A. baumannii including β-lactamases, multidrug efflux pumps and aminoglycoside-modifying enzymes. CONCLUSION The use of WGS for routine public health surveillance is a reliable method for the rapid detection of emerging AMR in A. baumannii isolates. Milk powder poses a risk to contain MDR Acinetobacter strains or resistance genes in Germany.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany; Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.
| | - Jörg Linde
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Philipp Hammer
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Kiel, Germany
| | - Ngoc H Nguyen
- The Center of Training and Direction of Healthcare Activities, General Hospital of Phutho, Vietnam; Department of Health, General Hospital of Phutho, Phutho, Vietnam
| | - Tuan N M Nguyen
- The Center of Training and Direction of Healthcare Activities, General Hospital of Phutho, Vietnam
| | - Wolf D Splettstoesser
- Department of Microbiology & Hygiene, LADR GmbH, Medical Laboratory Braunschweig, Germany
| | - Oliwia Makarewicz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany; Research Campus Infectognostics, Jena, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Lisa D Sprague
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany; Research Campus Infectognostics, Jena, Germany
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30
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García-Soto S, Abdel-Glil MY, Tomaso H, Linde J, Methner U. Emergence of Multidrug-Resistant Salmonella enterica Subspecies enterica Serovar Infantis of Multilocus Sequence Type 2283 in German Broiler Farms. Front Microbiol 2020; 11:1741. [PMID: 32765483 PMCID: PMC7380084 DOI: 10.3389/fmicb.2020.01741] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022] Open
Abstract
During the last decade, Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) has become more prevalent across Europe with an increased capability to persist in broiler farms. In this study, we aimed to identify potential genetic causes for the increased emergence and longer persistence of S. Infantis in German poultry farms by high-throughput-sequencing. Broiler derived S. Infantis strains from two decades, the 1990s (n = 12) and the 2010s (n = 18), were examined phenotypically and genotypically to detect potential differences responsible for increased prevalence and persistence. S. Infantis organisms were characterized by serotyping and determining antimicrobial susceptibility using the microdilution method. Genotypic characteristics were analyzed by whole genome sequencing (WGS) to detect antimicrobial resistance and virulence genes as well as plasmids. To detect possible clonal relatedness within S. Infantis organisms, 17 accessible genomes from previous studies about emergent S. Infantis were downloaded and analyzed using complete genome sequence of SI119944 from Israel as reference. In contrast to the broiler derived antibiotic-sensitive S. Infantis strains from the 1990s, the majority of strains from the 2010s (15 out of 18) revealed a multidrug-resistance (MDR) phenotype that encodes for at least three antimicrobials families: aminoglycosides [ant(3“)-Ia], sulfonamides (sul1), and tetracyclines [tet(A)]. Moreover, these MDR strains carry a virulence gene pattern missing in strains from the 1990s. It includes genes encoding for fimbriae clusters, the yersiniabactin siderophore, mercury and disinfectants resistance and toxin/antitoxin complexes. In depth genomic analysis confirmed that the 15 MDR strains from the 2010s carry a pESI-like megaplasmid with resistance and virulence gene patterns detected in the emerged S. Infantis strain SI119944 from Israel and clones inside and outside Europe. Genotyping analysis revealed two sequence types (STs) among the resistant strains from the 2010s, ST2283 (n = 13) and ST32 (n = 2). The sensitive strains from the 1990s, belong to sequence type ST32 (n = 10) and ST1032 (n = 2). Therefore, this study confirms the emergence of a MDR S. Infantis pESI-like clone of ST2283 in German broiler farms with presumably high tendency of dissemination. Further studies on the epidemiology and control of S. Infantis in broilers are needed to prevent the transfer from poultry into the human food chain.
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Affiliation(s)
- Silvia García-Soto
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
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31
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Gonzalez-Santamarina B, Busch A, Garcia-Soto S, Abdel-Glil MY, Linde J, Fries R, Meemken D, Hotzel H, Tomaso H. Draft genome sequence of multi-resistant Salmonella enterica subsp. enterica serovar Rissen strain 19CS0416 isolated from Vietnam reveals mcr-1 plasmid mediated resistance to colistin already in 2013. J Genomics 2020; 8:76-79. [PMID: 32817764 PMCID: PMC7425045 DOI: 10.7150/jgen.42790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/13/2020] [Indexed: 12/29/2022] Open
Abstract
We report the first draft genome sequence of a Salmonella strain with plasmid-mediated resistance to colistin encoded by mcr-1 gene in Vietnam. Salmonella enterica subsp. enterica serovar Rissen was isolated from a Vietnamese pig slaughterhouse in 2013. We can confirm that mcr-1 gene is identical to the first reported mcr-1 gene of the Escherichia coli strain SHP45, isolated in 2015 from a Chinese pig. The plasmid containing this gene in the strain 19CS0416 was highly related (96.86% identity) to the plasmid (pHNSHP45) contained in this Chinese strain. Moreover, this plasmid was determined to be 100% identical to a plasmid (p13P477T-7) belonging to an Escherichia coli (13P477T) found in Hong Kong during the same year in pigs. Our results will aid in understanding the dissemination of mcr-1 gene in East Asia, dating back to as early as 2013.
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Affiliation(s)
- Belen Gonzalez-Santamarina
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
| | - Anne Busch
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany.,Department of Anesthesiology and Intensive Care Medicine, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany
| | - Silvia Garcia-Soto
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
| | - Mostafa Y Abdel-Glil
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
| | - Jörg Linde
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
| | - Reinhard Fries
- Institute of Food Safety and Food Hygiene, Section Meat Hygiene, Freie Universität Berlin, Königsweg 67, 14163 Berlin, Germany
| | - Diana Meemken
- Institute of Food Safety and Food Hygiene, Section Meat Hygiene, Freie Universität Berlin, Königsweg 67, 14163 Berlin, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
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32
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Zoran T, Weber M, Springer J, White PL, Bauer J, Schober A, Löffler C, Seelbinder B, Hünniger K, Kurzai O, Scherag A, Schäuble S, Morton CO, Einsele H, Linde J, Löffler J. Treatment with etanercept and low monocyte concentration contribute to the risk of invasive aspergillosis in patients post allogeneic stem cell transplantation. Sci Rep 2019; 9:17231. [PMID: 31754120 PMCID: PMC6872713 DOI: 10.1038/s41598-019-53504-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/29/2019] [Indexed: 12/16/2022] Open
Abstract
Invasive aspergillosis (IA) is a life-threatening complication among allogeneic hematopoietic stem cell transplant (alloSCT) recipients. Despite well known risk factors and different available assays, diagnosis of invasive aspergillosis remains challenging. 103 clinical variables from patients with hematological malignancies and subsequent alloSCT were collected. Associations between collected variables and patients with (n = 36) and without IA (n = 36) were investigated by applying univariate and multivariable logistic regression. The predictive power of the final model was tested in an independent patient cohort (23 IA cases and 25 control patients). Findings were investigated further by in vitro studies, which analysed the effect of etanercept on A. fumigatus-stimulated macrophages at the gene expression and cytokine secretion. Additionally, the release of C-X-C motif chemokine ligand 10 (CXCL10) in patient sera was studied. Low monocyte concentration (p = 4.8 × 10−06), severe GvHD of the gut (grade 2–4) (p = 1.08 × 10−02) and etanercept treatment of GvHD (p = 3.5 × 10−03) were significantly associated with IA. Our studies showed that etanercept lowers CXCL10 concentrations in vitro and ex vivo and down-regulates genes involved in immune responses and TNF-alpha signaling. Our study offers clinicians new information regarding risk factors for IA including low monocyte counts and administration of etanercept. After necessary validation, such information may be used for decision making regarding antifungal prophylaxis or closely monitoring patients at risk.
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Affiliation(s)
- Tamara Zoran
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany.,Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Michael Weber
- Friedrich Löffler Institute, Institute of Molecular Pathogenesis, Jena, Germany.,Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Jan Springer
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | | | - Joachim Bauer
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | - Annika Schober
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | - Claudia Löffler
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | - Bastian Seelbinder
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Kerstin Hünniger
- Septomics Research Centre, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Oliver Kurzai
- Septomics Research Centre, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - André Scherag
- Institute of Medical Statistics, Computer and Data Sciences, University Hospital, Jena, Germany
| | - Sascha Schäuble
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - C Oliver Morton
- Western Sydney University, School of Science and Health, Campbelltown, NSW, 2560, Australia
| | - Hermann Einsele
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | - Jörg Linde
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Friedrich Löffler Institute, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Jürgen Löffler
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany.
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33
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Kofoed KF, Kelbaek H, Sigvardsen P, Torp-Pedersen C, Riis-Hansen P, Holmvang L, Elming H, Hofsten D, Engstroem T, Gislason G, Kober L, Linde J. 86Coronary CT angiography as the first-line diagnostic strategy in patients with non-ST-segment Elevation Acute Coronary Syndrome - The VERDICT trial. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz747.0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
In patients with non-ST segment elevation acute coronary syndrome (NSTE-ACS) coronary pathology may range from structurally normal vessels to severe coronary artery disease. Current guidelines recommend early invasive coronary angiography (ICA) to guide management strategy.
Purpose
We tested the hypothesis that a strategy of first-line coronary computed tomography angiography (CCTA) may be used to differentiate between significant and nonsignificant coronary artery stenosis in patients with NSTE-ACS.
Methods
We included patients with NSTE-ACS confirmed by ischaemic ECG changes and/or elevated biomarkers of myocardial ischaemia, in whom ICA was feasible within 12 hours. Patients were randomised 1:1 to ICA within 12 hours (Very Early) or 48–72 hours (Standard) and CCTA was conducted prior to ICA. The primary endpoint was the ability of CCTA to rule out significant coronary artery stenosis (≥50% stenosis) expressed as the negative predictive value (NPV) using ICA as the reference standard. The VERDICT trial is registered with ClinicalTrials.gov number NCT02061891.
Results
CCTA was conducted in 1023 patients – Very Early, 2.5 (IQR 1.8, 4.2) hours, N=583 and Standard, 59.9 (IQR 38.9, 86.7) hours, N=440 after establishment of the diagnosis. Significant coronary stenosis was found by ICA in 67.4% of the patients. NPV of CCTA (95% CI) was 90.9% (86.8%-94.1%) and the positive predictive value, sensitivity and specificity were 87.9% (85.3–90.1%), 96.5 (94.9–97.8%) and 72.4 (67.2–77.1%), respectively. False negative patients (24/1023, 2.3%) mostly had lesions in coronary segments with a luminal diameter ≤2.5 mm. NPV was not influenced by patient characteristics or clinical risk profile, including abnormal cardiac troponin, ischaemic ECG changes, or a GRACE risk score>140. CCTA accuracy parameters were similar in Very Early and the Standard strategy group.
Conclusions
First-line CCTA may be used to rule out clinically significant coronary artery disease in patients with NSTE-ACS and thus potentially guide patient management.
Acknowledgement/Funding
This study was funded by the Danish Agency for Science, Technology, and Innovation and the Danish Council for Strategic Research (grant no. 09–066994)
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Affiliation(s)
- K F Kofoed
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - H Kelbaek
- University Hospital, Roskilde, Denmark
| | - P Sigvardsen
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - L Holmvang
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - H Elming
- University Hospital, Roskilde, Denmark
| | - D Hofsten
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - T Engstroem
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - G Gislason
- Gentofte University Hospital, Gentofte, Denmark
| | - L Kober
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - J Linde
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
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34
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Kofoed KF, Engstroem T, Sigvardsen P, Torp-Pedersen C, Linde J, Riis Hansen P, Holmvang L, Hofsten D, Elming H, Gislason G, Kelbaek H, Kober L. 3335First-line coronary computed tomography predicts long-term clinical outcome in patients with Non-ST-segment elevation acute coronary syndrome - The VERDICT trial. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz745.0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
In patients with non-ST segment elevation acute coronary syndrome (NSTE-ACS) coronary pathology may range from structurally normal vessels to severe coronary artery disease. Current guidelines recommend early invasive coronary angiography (ICA) for risk assessment and choice of treatment strategy.
Purpose
We tested the hypothesis that 1) a first-line coronary computed tomography angiography (CCTA) predicts long term clinical outcome in patients with NSTE-ACS and 2) adding ICA to CCTA does not improve prediction of cardiovascular events.
Methods
We included patients with NSTE-ACS confirmed by ischaemic ECG changes and/or elevated biomarkers of myocardial ischaemia, in whom both CCTA and ICA were feasible within 12 hours. According to the VERDICT study protocol (ClinicalTrials.gov number NCT02061891) patients were randomised 1:1 to evaluation within 12 hours (Very Early) or 48–72 hours (Standard). CCTA was conducted prior to ICA and patients with an event between tests were excluded. Based on CCTA and ICA, patients were categorized according to European Society of Cardiology (ESC) guidelines as having prognostic indication for coronary revascularization ESCprog (left main stenosis, proximal left anterior descending artery stenosis or multivessel disease) or no prognostic indication – ESCnon-prog. The primary endpoint was a combined endpoint of all-cause mortality, non-fatal recurrent myocardial infarction, hospital admission for refractory myocardial ischemia or hospital admission for left sided heart failure. Discrimination of 1.5-year outcomes was assessed by time-dependent area under the receiver operating characteristic curve (AUC).
Results
CCTA and ICA was conducted in 979 patients. During a median follow-up time of 4.2 (IQR 2.7–5.5) years the primary endpoint occurred in 209 (21.3%) patients. Patients with ESCprog as defined by CCTA had a hazard ratio of 1.53 (95% CI 1.16–2.03) for occurrence of the primary endpoint. AUC for the prediction of the primary endpoint by CCTA was 68.6 (95% CI: 62.7–74.5) as compared to 68.6 (95% CI: 62.8–74.5), when adding ICA to the model. Similar findings were noted in patients randomized to either Very Early or Standard treatment strategy.
Conclusions
Long-term risk assessment in patients with NSTE-ACS may be conducted using a first-line CCTA strategy and may thus potentially guide patient management. Adding invasive coronary angiography to CCTA does not improve risk assessment.
Acknowledgement/Funding
This study was funded by the Danish Agency for Science, Technology, and Innovation and the Danish Council for Strategic Research (grant no. 09–066994)
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Affiliation(s)
- K F Kofoed
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - T Engstroem
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - P Sigvardsen
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | | | - J Linde
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | | | - L Holmvang
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - D Hofsten
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - H Elming
- University Hospital, Roskilde, Denmark
| | - G Gislason
- Gentofte University Hospital, Gentofte, Denmark
| | - H Kelbaek
- University Hospital, Roskilde, Denmark
| | - L Kober
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
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Kirtzel J, Madhavan S, Wielsch N, Blinne A, Hupfer Y, Linde J, Krause K, Svatoš A, Kothe E. Enzymatic Bioweathering and Metal Mobilization From Black Slate by the Basidiomycete Schizophyllum commune. Front Microbiol 2018; 9:2545. [PMID: 30405590 PMCID: PMC6207625 DOI: 10.3389/fmicb.2018.02545] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 10/05/2018] [Indexed: 11/21/2022] Open
Abstract
Schizophyllum commune is a filamentous basidiomycete causing white-rot in many wood species with the help of a broad range of enzymes including multicopper oxidases such as laccases and laccase-like oxidases. Since these enzymes exhibit a broad substrate range, their ability to oxidatively degrade black slate was investigated. Both haploid monokaryotic, and mated dikaryotic strains were able to grow on black slate rich in organic carbon as sole carbon source. On defined media, only the monokaryon showed growth promotion by addition of slate. At the same time, metals were released from the slate and, after reaching a threshold concentration, inhibited further growth of the fungus. The proteome during decomposition of the black slate showed induction of proteins potentially involved in rock degradation and stress resistance, and the gene for laccase-like oxidase mco2 was up-regulated. Specifically in the dikaryon, the laccase gene lcc1 was induced, while lcc2 as well as mco1, mco3, and mco4 expression levels remained similar. Spectrophotometric analysis revealed that both life forms were able to degrade the rock and produce smaller particles.
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Affiliation(s)
- Julia Kirtzel
- Microbial Communication, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Soumya Madhavan
- Microbial Communication, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Natalie Wielsch
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Yvonne Hupfer
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Katrin Krause
- Microbial Communication, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Erika Kothe
- Microbial Communication, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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36
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Conrad T, Kniemeyer O, Henkel SG, Krüger T, Mattern DJ, Valiante V, Guthke R, Jacobsen ID, Brakhage AA, Vlaic S, Linde J. Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC Syst Biol 2018; 12:88. [PMID: 30342519 PMCID: PMC6195963 DOI: 10.1186/s12918-018-0620-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/08/2018] [Indexed: 12/20/2022]
Abstract
Background Omics data provide deep insights into overall biological processes of organisms. However, integration of data from different molecular levels such as transcriptomics and proteomics, still remains challenging. Analyzing lists of differentially abundant molecules from diverse molecular levels often results in a small overlap mainly due to different regulatory mechanisms, temporal scales, and/or inherent properties of measurement methods. Module-detecting algorithms identifying sets of closely related proteins from protein-protein interaction networks (PPINs) are promising approaches for a better data integration. Results Here, we made use of transcriptome, proteome and secretome data from the human pathogenic fungus Aspergillus fumigatus challenged with the antifungal drug caspofungin. Caspofungin targets the fungal cell wall which leads to a compensatory stress response. We analyzed the omics data using two different approaches: First, we applied a simple, classical approach by comparing lists of differentially expressed genes (DEGs), differentially synthesized proteins (DSyPs) and differentially secreted proteins (DSePs); second, we used a recently published module-detecting approach, ModuleDiscoverer, to identify regulatory modules from PPINs in conjunction with the experimental data. Our results demonstrate that regulatory modules show a notably higher overlap between the different molecular levels and time points than the classical approach. The additional structural information provided by regulatory modules allows for topological analyses. As a result, we detected a significant association of omics data with distinct biological processes such as regulation of kinase activity, transport mechanisms or amino acid metabolism. We also found a previously unreported increased production of the secondary metabolite fumagillin by A. fumigatus upon exposure to caspofungin. Furthermore, a topology-based analysis of potential key factors contributing to drug-caused side effects identified the highly conserved protein polyubiquitin as a central regulator. Interestingly, polyubiquitin UbiD neither belonged to the groups of DEGs, DSyPs nor DSePs but most likely strongly influenced their levels. Conclusion Module-detecting approaches support the effective integration of multilevel omics data and provide a deep insight into complex biological relationships connecting these levels. They facilitate the identification of potential key players in the organism’s stress response which cannot be detected by commonly used approaches comparing lists of differentially abundant molecules. Electronic supplementary material The online version of this article (10.1186/s12918-018-0620-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- T Conrad
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
| | - O Kniemeyer
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | | | - T Krüger
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - D J Mattern
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Present address: PerkinElmer Inc., Rodgau, Germany
| | - V Valiante
- Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - R Guthke
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - I D Jacobsen
- Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - A A Brakhage
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - S Vlaic
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - J Linde
- Research Group PiDOMICs, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute for Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health - Friedrich Loeffler Institute, Jena, Germany
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37
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Sieber P, Voigt K, Kämmer P, Brunke S, Schuster S, Linde J. Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host Invasion. Front Microbiol 2018; 9:2313. [PMID: 30333805 PMCID: PMC6176087 DOI: 10.3389/fmicb.2018.02313] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/11/2018] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) is an important regulatory mechanism in eukaryotes but only little is known about its impact in fungi. Human fungal pathogens are of high clinical interest causing recurrent or life-threatening infections. AS can be well-investigated genome-wide and quantitatively with the powerful technology of RNA-Seq. Here, we systematically studied AS in human fungal pathogens based on RNA-Seq data. To do so, we investigated its effect in seven fungi during conditions simulating ex vivo infection processes and during in vitro stress. Genes undergoing AS are species-specific and act independently from differentially expressed genes pointing to an independent mechanism to change abundance and functionality. Candida species stand out with a low number of introns with higher and more varying lengths and more alternative splice sites. Moreover, we identified a functional difference between response to host and other stress conditions: During stress, AS affects more genes and is involved in diverse regulatory functions. In contrast, during response-to-host conditions, genes undergoing AS have membrane functionalities and might be involved in the interaction with the host. We assume that AS plays a crucial regulatory role in pathogenic fungi and is important in both response to host and stress conditions.
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Affiliation(s)
- Patricia Sieber
- Department of Bioinformatics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.,Research Group Systems Biology, Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Philipp Kämmer
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Sascha Brunke
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Jörg Linde
- Research Group PiDOMICS, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute for Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health-Friedrich-Loeffler-Institute, Jena, Germany
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38
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Schüttler C, Buschhüter N, Döllinger C, Ebert L, Hummel M, Linde J, Prokosch HU, Proynova R, Lablans M. [Erratum to: Requirements for a cross-location biobank IT infrastructure : Survey of stakeholder input on the establishment of a biobank network of the German Biobank Alliance (GBA)]. Pathologe 2018; 39:423. [PMID: 30105610 DOI: 10.1007/s00292-018-0479-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- C Schüttler
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wetterkreuz 13, 91058, Erlangen-Tennenlohe, Deutschland.
| | - N Buschhüter
- Zentralisierte Biomaterialbank der Medizinischen Fakultät der RWTH Aachen University, Aachen, Deutschland
| | - C Döllinger
- BioMaterialBank Heidelberg, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - L Ebert
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Heidelberg, Deutschland
| | - M Hummel
- Zentrale Biomaterialbank (ZeBanC) und German Biobank Node (GBN), Charité-Universitätsmedizin Berlin, Berlin, Deutschland
| | - J Linde
- UMG Biobank, Universitätsmedizin Göttingen, Göttingen, Deutschland
| | - H-U Prokosch
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wetterkreuz 13, 91058, Erlangen-Tennenlohe, Deutschland
| | - R Proynova
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Heidelberg, Deutschland
| | - M Lablans
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Heidelberg, Deutschland
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Bechsgaard DF, Gustafsson I, Michelsen MM, Mygind ND, Pena A, Raft KF, Linde J, Kofoed KF, Prescott E, Hove JD. P1783Women with angina and no obstructive coronary artery disease have reduced myocardial perfusion reserve assessed with cardiac computed tomography perfusion. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p1783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- D F Bechsgaard
- Hvidovre UniversityHospital, Cardiology, Copenhagen, Denmark
| | - I Gustafsson
- Hvidovre UniversityHospital, Cardiology, Copenhagen, Denmark
| | - M M Michelsen
- Bispebjerg University Hospital, Cardiology, Copenhagen, Denmark
| | - N D Mygind
- Rigshospitalet - Copenhagen University Hospital, Cardiology, Copenhagen, Denmark
| | - A Pena
- Gentofte University Hospital, Cardiology, Copenhagen, Denmark
| | - K F Raft
- Bispebjerg University Hospital, Cardiology, Copenhagen, Denmark
| | - J Linde
- Rigshospitalet - Copenhagen University Hospital, Cardiology, Copenhagen, Denmark
| | - K F Kofoed
- Rigshospitalet - Copenhagen University Hospital, Cardiology, Copenhagen, Denmark
| | - E Prescott
- Bispebjerg University Hospital, Cardiology, Copenhagen, Denmark
| | - J D Hove
- Hvidovre UniversityHospital, Cardiology, Copenhagen, Denmark
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40
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Schüttler C, Buschhüter N, Döllinger C, Ebert L, Hummel M, Linde J, Prokosch HU, Proynova R, Lablans M. Anforderungen an eine standortübergreifende Biobanken-IT-Infrastruktur. Pathologe 2018; 39:289-296. [DOI: 10.1007/s00292-018-0435-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Wolf T, Kämmer P, Brunke S, Linde J. Two's company: studying interspecies relationships with dual RNA-seq. Curr Opin Microbiol 2017; 42:7-12. [PMID: 28957710 DOI: 10.1016/j.mib.2017.09.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/24/2017] [Accepted: 09/01/2017] [Indexed: 01/03/2023]
Abstract
Organisms do not exist isolated from each other, but constantly interact. Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. Technological advances in next-generation sequencing over the recent years now allow us to apply RNA sequencing to two species at the same time (dual RNA-seq), and thus to directly study the gene expression of two interacting species without the need to physically separate cells or RNA. In this review, we give an overview over the latest studies in interspecies interactions made possible by dual RNA-seq, ranging from pathogenic to symbiotic relationships. We summarize state-of-the-art experimental techniques, bioinformatic data analysis and data interpretation, while also highlighting potential problems and pitfalls starting from the selection of meaningful time points and number of reads to matters of rRNA depletion. A short outlook on new trends in the field of dual RNA-seq concludes this review, looking at sequencing of non-coding RNAs during host-pathogen interactions and the prediction of molecular interspecies interactions networks.
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Affiliation(s)
- Thomas Wolf
- Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Philipp Kämmer
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Jörg Linde
- Research Group PiDOMICS, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany.
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Magnusson R, Mariotti GP, Köpsén M, Lövfors W, Gawel DR, Jörnsten R, Linde J, Nordling TEM, Nyman E, Schulze S, Nestor CE, Zhang H, Cedersund G, Benson M, Tjärnberg A, Gustafsson M. LASSIM-A network inference toolbox for genome-wide mechanistic modeling. PLoS Comput Biol 2017. [PMID: 28640810 PMCID: PMC5501685 DOI: 10.1371/journal.pcbi.1005608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets. The rationale behind LASSIM is that biological GRNs can be simplified using a limited subset of core genes that are assumed to regulate all other gene transcription events in the network. The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. As a method, LASSIM works in two steps, where it first infers a non-linear ODE system of the pre-specified core gene expression. Second, LASSIM in parallel optimizes the parameters that model the regulation of peripheral genes by core system genes. We showed the usefulness of this method by applying LASSIM to infer a large-scale non-linear model of naïve Th2 cell differentiation, made possible by integrating Th2 specific bindings, time-series together with six public and six novel siRNA-mediated knock-down experiments. ChIP-seq showed significant overlap for all tested transcription factors. Next, we performed novel time-series measurements of total T-cells during differentiation towards Th2 and verified that our LASSIM model could monitor those data significantly better than comparable models that used the same Th2 bindings. In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models with truly systems-level data. We demonstrate the power of this approach by inferring a mechanistically motivated, genome-wide model of the Th2 transcription regulatory system, which plays an important role in several immune related diseases. There are excellent methods to mathematically model time-resolved biological data on a small scale using accurate mechanistic models. Despite the rapidly increasing availability of such data, mechanistic models have not been applied on a genome-wide level due to excessive runtimes and the non-identifiability of model parameters. However, genome-wide, mechanistic models could potentially answer key clinical questions, such as finding the best drug combinations to induce an expression change from a disease to a healthy state. We present LASSIM, which is a toolbox built to infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the network inference into small solvable sub-problems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces computation time.
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Affiliation(s)
- Rasmus Magnusson
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Guido Pio Mariotti
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Mattias Köpsén
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - William Lövfors
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Danuta R. Gawel
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Rebecka Jörnsten
- Mathematical Sciences, Chalmers University of Technology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Linde
- Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Research Group Systems Biology and Bioinformatics, Jena, Germany
- Research Group PiDOMICS, Leibniz Institute for Natural Product Research and Infection Biology -Hans Knöll Institute, Jena, Germany
| | - Torbjörn E. M. Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan
- Stockholm Bioinformatics Center, Science for Life Laboratory, Solna, Sweden
| | - Elin Nyman
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Sylvie Schulze
- Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Research Group Systems Biology and Bioinformatics, Jena, Germany
| | - Colm E. Nestor
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Huan Zhang
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Gunnar Cedersund
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
- Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Mikael Benson
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Andreas Tjärnberg
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
- * E-mail:
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Schleicher J, Conrad T, Gustafsson M, Cedersund G, Guthke R, Linde J. Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions. Brief Funct Genomics 2017; 16:57-69. [PMID: 26857943 PMCID: PMC5439285 DOI: 10.1093/bfgp/elv064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent and rapidly evolving progress on high-throughput measurement techniques and computational performance has led to the emergence of new disciplines, such as systems medicine and translational systems biology. At the core of these disciplines lies the desire to produce multiscale models: mathematical models that integrate multiple scales of biological organization, ranging from molecular, cellular and tissue models to organ, whole-organism and population scale models. Using such models, hypotheses can systematically be tested. In this review, we present state-of-the-art multiscale modelling of bacterial and fungal infections, considering both the pathogen and host as well as their interaction. Multiscale modelling of the interactions of bacteria, especially Mycobacterium tuberculosis, with the human host is quite advanced. In contrast, models for fungal infections are still in their infancy, in particular regarding infections with the most important human pathogenic fungi, Candida albicans and Aspergillus fumigatus. We reflect on the current availability of computational approaches for multiscale modelling of host-pathogen interactions and point out current challenges. Finally, we provide an outlook for future requirements of multiscale modelling.
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Affiliation(s)
| | | | | | | | | | - Jörg Linde
- Corresponding author: Jörg Linde, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany. Tel.: +49-3641-532-1290; E-mail:
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Dix A, Czakai K, Leonhardt I, Schäferhoff K, Bonin M, Guthke R, Einsele H, Kurzai O, Löffler J, Linde J. Specific and Novel microRNAs Are Regulated as Response to Fungal Infection in Human Dendritic Cells. Front Microbiol 2017; 8:270. [PMID: 28280489 PMCID: PMC5322194 DOI: 10.3389/fmicb.2017.00270] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/08/2017] [Indexed: 11/15/2022] Open
Abstract
Within the last two decades, the incidence of invasive fungal infections has been significantly increased. They are characterized by high mortality rates and are often caused by Candida albicans and Aspergillus fumigatus. The increasing number of infections underlines the necessity for additional anti-fungal therapies, which require extended knowledge of gene regulations during fungal infection. MicroRNAs are regulators of important cellular processes, including the immune response. By analyzing their regulation and impact on target genes, novel therapeutic and diagnostic approaches may be developed. Here, we examine the role of microRNAs in human dendritic cells during fungal infection. Dendritic cells represent the bridge between the innate and the adaptive immune systems. Therefore, analysis of gene regulation of dendritic cells is of particular significance. By applying next-generation sequencing of small RNAs, we quantify microRNA expression in monocyte-derived dendritic cells after 6 and 12 h of infection with C. albicans and A. fumigatus as well as treatment with lipopolysaccharides (LPS). We identified 26 microRNAs that are differentially regulated after infection by the fungi or LPS. Three and five of them are specific for fungal infections after 6 and 12 h, respectively. We further validated interactions of miR-132-5p and miR-212-5p with immunological relevant target genes, such as FKBP1B, KLF4, and SPN, on both RNA and protein level. Our results indicate that these microRNAs fine-tune the expression of immune-related target genes during fungal infection. Beyond that, we identified previously undiscovered microRNAs. We validated three novel microRNAs via qRT-PCR. A comparison with known microRNAs revealed possible relations with the miR-378 family and miR-1260a/b for two of them, while the third one features a unique sequence with no resemblance to known microRNAs. In summary, this study analyzes the effect of known microRNAs in dendritic cells during fungal infections and proposes novel microRNAs that could be experimentally verified.
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Affiliation(s)
- Andreas Dix
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany
| | - Kristin Czakai
- Department of Internal Medicine II, University Hospital of Würzburg Würzburg, Germany
| | - Ines Leonhardt
- Septomics Research Centre, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Friedrich Schiller UniversityJena, Germany; IMGM Laboratories GmbHMartinsried, Germany
| | - Karin Schäferhoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen Tübingen, Germany
| | | | - Reinhard Guthke
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital of Würzburg Würzburg, Germany
| | - Oliver Kurzai
- Septomics Research Centre, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Friedrich Schiller UniversityJena, Germany; Center for Sepsis Control and Care, University HospitalJena, Germany; Institute for Microbiology, University of WuerzburgWuerzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, University Hospital of Würzburg Würzburg, Germany
| | - Jörg Linde
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany
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Ko B, Linde J, Ihdayhid A, Norgaard B, Kofoed K, Sørgaard M, Leipsic J, Munnur R, Adams D, Laggoune J, Crossett M, Cameron J, Wong D, Seneviratne S. Diagnostic Performance of CT-Derived Fractional Flow Reserve using Three Dimensional Fluid Modelling and CT Stress Myocardial Perfusion Imaging for Detection of Haemodynamically Significant Coronary Stenosis. Heart Lung Circ 2017. [DOI: 10.1016/j.hlc.2017.06.491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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Ihdayhid A, Sakaguchi T, Linde J, Sørgaard M, Kofoed K, Fujisawa Y, Hislop-Jambrich J, Nerlekar N, Cameron J, Munnur R, Wong D, Seneviratne S, Ko B. Diagnostic Performance of CT Derived Fractional Flow Reserve Using Reduced Order Modelling and CT Stress Myocardial Perfusion Imaging for Detection of Haemodynamically Significant Coronary Stenosis. Heart Lung Circ 2017. [DOI: 10.1016/j.hlc.2017.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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47
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Hebecker B, Vlaic S, Conrad T, Bauer M, Brunke S, Kapitan M, Linde J, Hube B, Jacobsen ID. Corrigendum: Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions. Sci Rep 2016; 6:39423. [PMID: 27991566 PMCID: PMC5172156 DOI: 10.1038/srep39423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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48
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Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K. Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina). PLoS Genet 2016; 12:e1006491. [PMID: 27918580 PMCID: PMC5137873 DOI: 10.1371/journal.pgen.1006491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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49
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Hebecker B, Vlaic S, Conrad T, Bauer M, Brunke S, Kapitan M, Linde J, Hube B, Jacobsen ID. Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions. Sci Rep 2016; 6:36055. [PMID: 27808111 PMCID: PMC5093689 DOI: 10.1038/srep36055] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/11/2016] [Indexed: 11/15/2022] Open
Abstract
Candida albicans is a common cause of life-threatening fungal bloodstream infections. In the murine model of systemic candidiasis, the kidney is the primary target organ while the fungal load declines over time in liver and spleen. To better understand these organ-specific differences in host-pathogen interaction, we performed gene expression profiling of murine kidney, liver and spleen and determined the fungal transcriptome in liver and kidney. We observed a delayed transcriptional immune response accompanied by late induction of fungal stress response genes in the kidneys. In contrast, early upregulation of the proinflammatory response in the liver was associated with a fungal transcriptome resembling response to phagocytosis, suggesting that phagocytes contribute significantly to fungal control in the liver. Notably, C. albicans hypha-associated genes were upregulated in the absence of visible filamentation in the liver, indicating an uncoupling of gene expression and morphology and a morphology-independent effect by hypha-associated genes in this organ. Consistently, integration of host and pathogen transcriptional data in an inter-species gene regulatory network indicated connections of C. albicans cell wall remodelling and metabolism to the organ-specific immune responses.
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Affiliation(s)
- Betty Hebecker
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena, Germany.,Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Sebastian Vlaic
- Department of General, Visceral and Vascular Surgery, Experimental Transplantation Surgery, Jena University Hospital, Jena, Germany.,Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena, Germany.,Department of Bioinformatics, Friedrich-Schiller-University Jena, Germany
| | - Theresia Conrad
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena, Germany
| | - Michael Bauer
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany.,Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena, Germany
| | - Mario Kapitan
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena, Germany
| | - Jörg Linde
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena, Germany
| | - Bernhard Hube
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany.,Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena, Germany.,Friedrich-Schiller-University, Jena, Germany
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena, Germany.,Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany.,Friedrich-Schiller-University, Jena, Germany
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50
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Freihorst D, Brunsch M, Wirth S, Krause K, Kniemeyer O, Linde J, Kunert M, Boland W, Kothe E. Smelling the difference: Transcriptome, proteome and volatilome changes after mating. Fungal Genet Biol 2016; 112:2-11. [PMID: 27593501 DOI: 10.1016/j.fgb.2016.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/24/2016] [Accepted: 08/30/2016] [Indexed: 10/21/2022]
Abstract
Mushrooms, such as Schizophyllum commune, have a specific odor. Whether this is linked to mating, prerequisite for mushroom formation, or also found in monokaryotic, unmated strains, was investigated with a comprehensive study on the transcriptome and proteome of this model organism. Mating interactions were investigated using a complete, cytosolic proteome map for unmated, monokaryotic, as well as for mated, dikaryotic mycelia. The regulations of the proteome were compared to transcriptional changes upon mating and to changes in smell by volatilome studies. We could show a good overlap between proteome and transcriptome data, but extensive posttranslational regulation was identified for more than 80% of transcripts. This suggests down-stream regulation upon interaction of mating partners and formation of the dikaryon that is competent to form fruiting bodies. The volatilome was shown to respond to mating by a broader spectrum of volatiles and increased emission of the mushroom smell molecules 3-octanone and 1-octen-3-ol, as well as ethanol and β-bisabolol in the dikaryon. Putatively involved biosynthetic proteins like alcohol dehydrogenases, Ppo-like oxygenases, or sesquiterpene synthases showed correlating transcriptional regulation depending on either mono- or dikaryotic stages.
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Affiliation(s)
- Daniela Freihorst
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany
| | - Melanie Brunsch
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany
| | - Sophia Wirth
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany
| | - Katrin Krause
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Jörg Linde
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Maritta Kunert
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Wilhelm Boland
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Erika Kothe
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany.
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